[petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!
Fande Kong
fdkong.jd at gmail.com
Wed Mar 10 17:21:22 CST 2021
On Wed, Mar 10, 2021 at 1:36 PM Satish Balay <balay at mcs.anl.gov> wrote:
> Can you use a different MPI for this conda install?
>
We control how to build MPI. If I take "-pie" options out of LDFLAGS, conda
can not compile mpich.
>
> Alternative:
>
> ./configure CC=x86_64-apple-darwin13.4.0-clang COPTFLAGS="-march=core2
> -mtune=haswell" CPPFLAGS=-I/Users/kongf/miniconda3/envs/testpetsc/include
> LDFLAGS="-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs
> -Wl,-commons,use_dylibs"
> LIBS="-Wl,-rpath,/Users/kongf/miniconda3/envs/testpetsc/lib -lmpi -lpmpi"
>
MPI can not generate an executable because we took out "-pie".
Thanks,
Fande
>
> etc.. [don't know if you really need LDFLAGS options]
>
> Satish
>
> On Wed, 10 Mar 2021, Fande Kong wrote:
>
> > I guess it was encoded in mpicc
> >
> > petsc % mpicc -show
> > x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -Wl,-pie
> > -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs
> > -Wl,-rpath,/Users/kongf/miniconda3/envs/testpetsc/lib
> > -L/Users/kongf/miniconda3/envs/testpetsc/lib -Wl,-commons,use_dylibs
> > -I/Users/kongf/miniconda3/envs/testpetsc/include
> > -L/Users/kongf/miniconda3/envs/testpetsc/lib -lmpi -lpmpi
> >
> >
> > Thanks,
> >
> > Fande
> >
> > On Wed, Mar 10, 2021 at 12:51 PM Satish Balay <balay at mcs.anl.gov> wrote:
> >
> > > > LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs
> -rpath
> > > /Users/kongf/miniconda3/envs/testpetsc/lib
> > > -L/Users/kongf/miniconda3/envs/testpetsc/lib
> > >
> > > Does conda compiler pick up '-pie' from this env variable? If so -
> perhaps
> > > its easier to just modify it?
> > >
> > > Or is it encoded in mpicc wrapper? [mpicc -show]
> > >
> > > Satish
> > >
> > > On Wed, 10 Mar 2021, Fande Kong wrote:
> > >
> > > > Thanks Barry,
> > > >
> > > > Got the same result, but "-pie" was not filtered out somehow.
> > > >
> > > > I did changes like this:
> > > >
> > > > kongf at x86_64-apple-darwin13 petsc % git diff
> > > > diff --git a/config/BuildSystem/config/framework.py
> > > > b/config/BuildSystem/config/framework.py
> > > > index beefe82956..c31fbeb95e 100644
> > > > --- a/config/BuildSystem/config/framework.py
> > > > +++ b/config/BuildSystem/config/framework.py
> > > > @@ -504,6 +504,8 @@ class Framework(config.base.Configure,
> > > > script.LanguageProcessor):
> > > > lines = [s for s in lines if s.find('Load a valid targeting
> module or
> > > > set CRAY_CPU_TARGET') < 0]
> > > > # pgi dumps filename on stderr - but returns 0 errorcode'
> > > > lines = [s for s in lines if lines != 'conftest.c:']
> > > > + # in case -pie is always being passed to linker
> > > > + lines = [s for s in lines if s.find('-pie being ignored. It is
> only
> > > > used when linking a main executable') < 0]
> > > > if lines: output = reduce(lambda s, t: s+t, lines, '\n')
> > > > else: output = ''
> > > > log.write("Linker stderr after filtering:\n"+output+":\n")
> > > >
> > > > The log was attached again.
> > > >
> > > > Thanks,
> > > >
> > > > Fande
> > > >
> > > >
> > > > On Wed, Mar 10, 2021 at 12:05 PM Barry Smith <bsmith at petsc.dev>
> wrote:
> > > >
> > > > > Fande,
> > > > >
> > > > > Please add in config/BuildSystem/config/framework.py line 528
> two
> > > new
> > > > > lines
> > > > >
> > > > > # pgi dumps filename on stderr - but returns 0 errorcode'
> > > > > lines = [s for s in lines if lines != 'conftest.c:']
> > > > > # in case -pie is always being passed to linker
> > > > > lines = [s for s in lines if s.find('-pie being ignored. It
> is
> > > only
> > > > > used when linking a main executable') < 0]
> > > > >
> > > > > Barry
> > > > >
> > > > > You have (another of Conda's "take over the world my way"
> approach)
> > > > >
> > > > > LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs
> > > -rpath
> > > > > /Users/kongf/miniconda3/envs/testpetsc/lib
> > > > > -L/Users/kongf/miniconda3/envs/testpetsc/lib
> > > > >
> > > > > Executing: mpicc -o
> > > > >
> > >
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/conftest
> > > > > -dynamiclib -single_module
> > > > >
> > >
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/conftest.o
> > > > > Possible ERROR while running linker:
> > > > > stderr:
> > > > > ld: warning: -pie being ignored. It is only used when linking a
> main
> > > > > executable
> > > > > Rejecting C linker flag -dynamiclib -single_module due
> to
> > > > >
> > > > > ld: warning: -pie being ignored. It is only used when linking a
> main
> > > > > executable
> > > > >
> > > > > This is the correct link command for the Mac but it is being
> rejected
> > > due
> > > > > to the warning message.
> > > > >
> > > > >
> > > > > On Mar 10, 2021, at 10:11 AM, Fande Kong <fdkong.jd at gmail.com>
> wrote:
> > > > >
> > > > > Thanks, Barry,
> > > > >
> > > > > It seems PETSc works fine with manually built compilers. We are
> pretty
> > > > > much sure that the issue is related to conda. Conda might introduce
> > > extra
> > > > > flags.
> > > > >
> > > > > We still need to make it work with conda because we deliver our
> package
> > > > > via conda for users.
> > > > >
> > > > >
> > > > > I unset all flags from conda, and got slightly different results
> this
> > > > > time. The log was attached. Anyone could explain the motivation
> that
> > > we
> > > > > try to build executable without a main function?
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Fande
> > > > >
> > > > > Executing: mpicc -c -o
> > > > >
> > >
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/conftest.o
> > > > >
> > >
> -I/var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers
> > > > > -fPIC
> > > > >
> > >
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/conftest.c
> > > > >
> > > > > Successful compile:
> > > > > Source:
> > > > > #include "confdefs.h"
> > > > > #include "conffix.h"
> > > > > #include <stdio.h>
> > > > > int (*fprintf_ptr)(FILE*,const char*,...) = fprintf;
> > > > > void foo(void){
> > > > > fprintf_ptr(stdout,"hello");
> > > > > return;
> > > > > }
> > > > > void bar(void){foo();}
> > > > > Running Executable WITHOUT threads to time it out
> > > > > Executing: mpicc -o
> > > > >
> > >
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/libconftest.so
> > > > > -dynamic -fPIC
> > > > >
> > >
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-pkset22y/config.setCompilers/conftest.o
> > > > >
> > > > > Possible ERROR while running linker: exit code 1
> > > > > stderr:
> > > > > Undefined symbols for architecture x86_64:
> > > > > "_main", referenced from:
> > > > > implicit entry/start for main executable
> > > > > ld: symbol(s) not found for architecture x86_64
> > > > > clang-11: error: linker command failed with exit code 1 (use -v to
> see
> > > > > invocation)
> > > > > Rejected C compiler flag -fPIC because it was not
> compatible
> > > > > with shared linker mpicc using flags ['-dynamic']
> > > > >
> > > > >
> > > > > On Mon, Mar 8, 2021 at 7:28 PM Barry Smith <bsmith at petsc.dev>
> wrote:
> > > > >
> > > > >>
> > > > >> Fande,
> > > > >>
> > > > >> I see you are using CONDA, this can cause issues since it
> sticks
> > > all
> > > > >> kinds of things into the environment. PETSc tries to remove some
> of
> > > them
> > > > >> but perhaps not enough. If you run printenv you will see all the
> mess
> > > it is
> > > > >> dumping in.
> > > > >>
> > > > >> Can you trying the same build without CONDA environment?
> > > > >>
> > > > >> Barry
> > > > >>
> > > > >>
> > > > >> On Mar 8, 2021, at 7:31 PM, Matthew Knepley <knepley at gmail.com>
> > > wrote:
> > > > >>
> > > > >> On Mon, Mar 8, 2021 at 8:23 PM Fande Kong <fdkong.jd at gmail.com>
> > > wrote:
> > > > >>
> > > > >>> Thanks Matthew,
> > > > >>>
> > > > >>> Hmm, we still have the same issue after shutting off all unknown
> > > flags.
> > > > >>>
> > > > >>
> > > > >> Oh, I was misinterpreting the error message:
> > > > >>
> > > > >> ld: can't link with a main executable file
> > > > >>
> > >
> '/var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-6v1w4q4u/config.setCompilers/libconftest.dylib'
> > > > >>
> > > > >> So clang did not _actually_ make a shared library, it made an
> > > executable.
> > > > >> Did clang-11 change the options it uses to build a shared library?
> > > > >>
> > > > >> Satish, do we test with clang-11?
> > > > >>
> > > > >> Thanks,
> > > > >>
> > > > >> Matt
> > > > >>
> > > > >> Thanks,
> > > > >>>
> > > > >>> Fande
> > > > >>>
> > > > >>> On Mon, Mar 8, 2021 at 6:07 PM Matthew Knepley <
> knepley at gmail.com>
> > > > >>> wrote:
> > > > >>>
> > > > >>>> On Mon, Mar 8, 2021 at 7:55 PM Fande Kong <fdkong.jd at gmail.com>
> > > wrote:
> > > > >>>>
> > > > >>>>> Hi All,
> > > > >>>>>
> > > > >>>>> mpicc rejected "-fPIC". Anyone has a clue how to work around
> this
> > > > >>>>> issue?
> > > > >>>>>
> > > > >>>>
> > > > >>>> The failure is at the last step
> > > > >>>>
> > > > >>>> Executing: mpicc -o
> > > > >>>>
> > >
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-6v1w4q4u/config.setCompilers/conftest
> > > > >>>> -fPIC
> > > > >>>>
> > >
> /var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-6v1w4q4u/config.setCompilers/conftest.o
> > > > >>>>
> > >
> -L/var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-6v1w4q4u/config.setCompilers
> > > > >>>> -lconftest
> > > > >>>> Possible ERROR while running linker: exit code 1
> > > > >>>> stderr:
> > > > >>>> ld: can't link with a main executable file
> > > > >>>>
> > >
> '/var/folders/tv/ljnkj46x3nq45cp9tbkc000c0000gn/T/petsc-6v1w4q4u/config.setCompilers/libconftest.dylib'
> > > > >>>> for architecture x86_64
> > > > >>>> clang-11: error: linker command failed with exit code 1 (use -v
> to
> > > see
> > > > >>>> invocation)
> > > > >>>>
> > > > >>>> but you have some flags stuck in which may or may not affect
> this. I
> > > > >>>> would try shutting them off:
> > > > >>>>
> > > > >>>> LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs
> > > -rpath
> > > > >>>> /Users/kongf/miniconda3/envs/moose/lib
> > > > >>>> -L/Users/kongf/miniconda3/envs/moose/lib
> > > > >>>>
> > > > >>>> I cannot tell exactly why clang is failing because it does not
> > > report a
> > > > >>>> specific error.
> > > > >>>>
> > > > >>>> Thanks,
> > > > >>>>
> > > > >>>> Matt
> > > > >>>>
> > > > >>>> The log was attached.
> > > > >>>>>
> > > > >>>>> Thanks so much,
> > > > >>>>>
> > > > >>>>> Fande
> > > > >>>>>
> > > > >>>>
> > > > >>>>
> > > > >>>> --
> > > > >>>> What most experimenters take for granted before they begin their
> > > > >>>> experiments is infinitely more interesting than any results to
> > > which their
> > > > >>>> experiments lead.
> > > > >>>> -- Norbert Wiener
> > > > >>>>
> > > > >>>> https://www.cse.buffalo.edu/~knepley/
> > > > >>>> <http://www.cse.buffalo.edu/~knepley/>
> > > > >>>>
> > > > >>>
> > > > >>
> > > > >> --
> > > > >> What most experimenters take for granted before they begin their
> > > > >> experiments is infinitely more interesting than any results to
> which
> > > their
> > > > >> experiments lead.
> > > > >> -- Norbert Wiener
> > > > >>
> > > > >> https://www.cse.buffalo.edu/~knepley/
> > > > >> <http://www.cse.buffalo.edu/~knepley/>
> > > > >>
> > > > >>
> > > > >> <configure.log>
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>
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